Distinct BK polyomavirus non-coding control region (NCCR) variants in oral fluids of HIV- associated Salivary Gland Disease patients

Burger-Calderon, Raquel; Ramsey, Kathy; Dolittle-Hall, Janet M.; Seaman, William T.; Jeffers-Francis, Liesl K.; Tesfu, Daniel; Nickeleit, Volker; Webster‐Cyriaque, Jennifer

doi:10.1016/j.virol.2016.03.020

Cited by 13 publications

(25 citation statements)

References 70 publications

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“…The early region encodes the large T antigen (TAg), the small t antigens (tAg) and the short t antigen proteins. Hence the late region encodes VP1, VP2, VP3 structural proteins and a non-structural protein called agnoprotein (16)(17)(18)(19)(20)(21)(22)(23). BK polyomavirus can also be classified based on nongenetic and serological testing into several genotypes.…”

Section: Introductionmentioning

confidence: 99%

“…Loci polymorphisms in the noncoding control region (NCCR) genome of the virus has been reported. Substitutions and changes in some specific nucleotides in the genome of the virus can alter the amino acid residues in the protein core, and this change may play an important role in the pathogenesis, characteristics, and survival of the virus (16)(17)(18)(19)(20)(21)(22)(23). Few studies that examined the entire genome of BK polyomavirus have been done in the world.…”

Section: Introductionmentioning

confidence: 99%

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The complete genome sequence BK polyomavirus study in kidney transplanted patients

et al. 2018

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Background: BK polyomavirus is a member of the Polyomaviridae. This virus has spread worldwide and up to 82% of the world populations are serologically positive. BK polyomavirus usually transmits through inhalation or fecal-oral way in childhood, as well as is likely to cause an asymptomatic disease. The virus can be reactivated in people who are immunocompromised. Objectives: In this study we aimed to determine the complete genome sequence of BK polyomavirus in 5 patients receiving kidney transplantation in Golestan hospital, Ahvaz, south west of Iran. Materials and Methods: The study was performed on urine and blood samples from kidney transplant ward, Golestan hospital, Ahvaz, Iran. To amplify the whole genome of BK polyomavirus AccuPower ProFi Taq PCR PreMix kit (Bioneer, South Korea) was used. Then, purified fragments were cloned into the vector. Sequences derived from the sequencing process were assembled by MEGA7 software. Data were analyzed using MEGA7 software and a phylogenetic tree was built based on the maximum likelihood ratio method. Results: Overall, 40 urine samples (40%) and two plasma samples (12%) were positive for BK virus DNA. For the selected samples, W.G. Long PCR was performed and 5.1 kbp fragment was observed in all five samples. These fragments were cloned and sequenced. Genomic sequence analysis of the 5 strains studied showed 97.6% homology and all our study samples were of the same clade, which could be a reason for our patients to be infected with the same strain. Comparing the 5 isolates in our study with reference strains, showed more than 98% of homology, and variation was observed in less than 2% of nucleotides. Conclusion: These five isolates showed more than 98% homology compared to the reference sequences, which can be attributed to the fact that these patients are infected with a common strain or that the genomic stability in the strain exists in our geographic area. We can conclude that in our geographic region there is a genomic stability and this strain can also be used as a positive control sample in other parts of the country.

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

The complete genome sequence BK polyomavirus study in kidney transplanted patients

et al. 2018

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“…Over the years, several original works have tackled the content and diversity of the OPQRS block [5,7,31,32]. Initially, Markowitz et al defined nucleotide block length as per P(68), Q(39), and R(63) [31].…”

Section: Defining a Canon For The Archetypical Opqrs Blocksmentioning

confidence: 99%

“…The block length defined by Moens et al using 18 sequence consensus is O(142), P(68), Q(39), R(63), and S(63) [33], albeit it is also stated as a P(68) for the archetypical polyomavirus BK MM strain [32]. Later, Burger-Calderón et al stated the block length as O(142), P(70), Q(39), R(40), and S(64) [7]. Here we propose a variant for the arbitrary classification of the NCCR blocks, considering preceding efforts, in order to improve, automatize and harmonize its typing.…”

Section: Defining a Canon For The Archetypical Opqrs Blocksmentioning

confidence: 99%

“…NCCR is a bidirectional promoter-enhancer region that includes binding sites for several transcription factors [4]. The NCCR is known to be formed by repeat-rich regions, being highly variable in sequence and length [5][6][7]. Strains with NCCR rearrangements (i.e., deletions, insertions, or duplications of complete or partial blocks) are found in patients suffering from BKPyV disease.…”

Section: Introductionmentioning

confidence: 99%

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BKTyper: Free Online Tool for Polyoma BK Virus VP1 and NCCR Typing

Martí-Carreras

Mineeva-Sangwo

Topalis

et al. 2020

Viruses

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Human BK polyomavirus (BKPyV) prevalence has been increasing due to the introduction of more potent immunosuppressive agents in transplant recipients, and its clinical interest. BKPyV has been linked mostly to polyomavirus-associated hemorrhagic cystitis, in allogenic hematopoietic stem cell transplant, and polyomavirus-associated nephropathy in kidney transplant patients. BKPyV is a circular double-stranded DNA virus that encodes for seven proteins, of which Viral Protein 1 (VP1), the major structural protein, has been extensively used for genotyping. BKPyV also contains the noncoding control region (NCCR), configured by five repeat blocks (OPQRS) known to be highly repetitive and diverse, and linked to viral infectivity and replication. BKPyV genetic diversity has been mainly studied based on the NCCR and VP1, due to the high occurrence of BKPyV-associated diseases in transplant patients and their clinical implications. Here BKTyper is presented, a free online genotyper for BKPyV, based on a VP1 genotyping and a novel algorithm for NCCR block identification. VP1 genotyping is based on a modified implementation of the BK typing and grouping regions (BKTGR) algorithm, providing a maximum-likelihood phylogenetic tree using a custom internal BKPyV database. Novel NCCR block identification relies on a minimum of 12-bp motif recognition and a novel sorting algorithm. A graphical representation of the OPQRS block organization is provided.

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Phylogenetic analysis of BKV genetic variations, based on the whole sequence of the genome and different genomic sections

Baghi

Harzandi

Moniri

et al. 2022

Journal of Medical Virology

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BK polyomavirus (BKV) primarily infects humans in their early life stages, and in later life stages, immunosuppressed patients may develop asymptomatic infections. The nucleotides 1744-1812 in the VP1 gene are traditionally used to determine this virus's genotype. The complete genome of the BKV samples from patients referred to Masih Daneshvari Hospital's Virology Research Center was amplified by previously known primer sets. The phylogenetic diversity of the whole genome, different genomic sections, and the noncoding control region of BKV samples were investigated. Using software Mega X and references, the samples' genotype was determined in separate genomic fragments and the whole genome. The samples were classified into two genotypes (I and IV) and five subtypes (Ia, Ib-1, Ib-2, IVc-1, and IVc-2), but none of the isolates belonged to genotypes II, III, V, or VI. The large T antigen-based phylogenetic tree provided 100% bootstrap values for these divisions, which were superior to those (96%-100%) used in the VP1 sequence. Among the genomic segments, large tumor antigen and VP1 had the most mutations. The noncoding control area contained mutations at the O41 position in the granulocyte/macrophage stimulus gene and the P31 position in the NF-1 gene. The validity of the phylogenetic analysis was supported by sequence analysis, which found single-nucleotide polymorphisms (SNPs) that could be useful for subclassifying isolates.More research with a large number of samples and in the wider geographical areas is needed to understand the genetic diversity of the BKV in Iran and also to determine these SNPs' clinical significance in terms of patient outcome and viral load dynamics.

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Distinct BK polyomavirus non-coding control region (NCCR) variants in oral fluids of HIV- associated Salivary Gland Disease patients

Cited by 13 publications

References 70 publications

The complete genome sequence BK polyomavirus study in kidney transplanted patients

The complete genome sequence BK polyomavirus study in kidney transplanted patients

BKTyper: Free Online Tool for Polyoma BK Virus VP1 and NCCR Typing

Phylogenetic analysis of BKV genetic variations, based on the whole sequence of the genome and different genomic sections

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